While estate taxes motivated the DOMA case, in which Edith Windsor sued the federal government because her wife's estate had to pay more than $363,000 in estate taxes, less than 0.2 percent of estates are big enough to owe tax.

An estate may claim an unlimited spousal exemption for inherited assets up to $5.25 million. Any unused part of that limited exemption carries over to the estate of the surviving spouse, guaranteeing that $10.5 million of the couple's combined assets will go tax-free to the heirs.

Questions about the Supreme Court's decision will continue to be raised in the days to come.

Thomas Spychalski, partner with accounting and business advisory firm ParenteBeard, said same-sex couples should consult with tax and legal advisors as federal treatment regarding income and estate taxes varies from state recognition to non-recognition of same-sex marriages. Since the decision applies to states that recognize same-sex marriage, it is not clear what may happen if same-sex married couples move to a non-recognition state, he said.

Henry Guberman, another partner with ParenteBeard, said same-sex couples who are now eligible to file joint federal tax returns should consider "common pitfalls."

Same-sex couples, like heterosexual couples, should determine whether to file their tax returns as married filing jointly and married filing separately depending on which filing status reduces combined income taxes, he said.

"This is generally recommended when each party earns approximately the same income. Combining individual incomes can put the combined income into a higher tax bracket compared to filing separately," Guberman said.